Register on PhytoBacExplorer (https://phytobacexplorer.warwick.ac.uk/).
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After successful registration, we explore some of the most important aspects of the landing page:
As an example we will load Xanthomonas vasicola. You can choose any other target and neighbour (= off-targets) species.
In the example, our target is vasculorum. Our neighbours are all other Xv assemblies that are not vasculorum on PhytoBacExplorer.
Other options for Field in the Strain Metadata tab include:
Other Operator options include:
Field contains the ValueValue field will open a dialogue which allows you to insert lists of values separated by comma or whitespace.Field does not contain the ValueField is exactly what is defined in ValueField is not exactly what is defined in ValueBelow that, the AND button will allow you to search the same or different Fields that are contain, not contain etc. values. Entries returned will have to fullfill all defined criteria
This means that when you search for two different species using
ANDno entries will be returned because there are no entries that are two different species at the same time
Alternatively, you can use the OR button, which will return any entrie that has a Field of a certain Value or other Fields and Valuess.
For instance you, you can search for entries that are fragariae or campestris, which will return all assemblies that are fragariae and all that are campestris
then, in the top right corner we change Experimental Data to “Almeida_6_gene_MLST” and click the Grape Tree symbol:
The Create GrapeTree dialogue opens and we can give the tree a name, as well as chose between minimum spanning tree algorithms or neighbourhood joining algorithms. Both generate trees based on MLST allelic profiles 1.
Since we do not have missing data (all entries have defined STs), I chose a simple NJ algorithm (Ninja NJ).
Suggestion: if you want to, try out multiple different algorithms and compare topology.
We can annotate our tree by clicking on the legend and choosing which metadata we want to colour it by:
Suggestion: try colouring by other metadata, like country, too.
We can also annotate the nodes and show their labels. We are interested in the STs:
Our target STs in the Example are 67, 138 and 399.
We can press Shift and click on the nodes to select them. Then we can click Load Selected in the left panel.
We then see the metadata of all the strains.
We can right-click > select all again and then download the selected target assemblies for further downstream processing:
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compare https://enterobase.readthedocs.io/en/latest/grapetree/tutorial-2.html?highlight=grape%20tree and Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico, M Achtman (2018) “GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens”, Genome Res. doi: https://doi.org/10.1101/gr.232397.117↩︎